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gerrit-public.fairphone.software / platform / external / python / google-api-python-client / b8458c0b73030155b64a3c2392b2f70e5fbc3baf / . / docs / dyn / genomics_v1.readgroupsets.coveragebuckets.html
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Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]1<html><body>
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75<h1><a href="genomics_v1.html">Genomics API</a> . <a href="genomics_v1.readgroupsets.html">readgroupsets</a> . <a href="genomics_v1.readgroupsets.coveragebuckets.html">coveragebuckets</a></h1>
76<h2>Instance Methods</h2>
77<p class="toc_element">
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame]78 <code><a href="#list">list(readGroupSetId, targetBucketWidth=None, x__xgafv=None, end=None, start=None, referenceName=None, pageToken=None, pageSize=None)</a></code></p>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]79<p class="firstline">Lists fixed width coverage buckets for a read group set, each of which</p>
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]80<p class="toc_element">
81 <code><a href="#list_next">list_next(previous_request, previous_response)</a></code></p>
82<p class="firstline">Retrieves the next page of results.</p>
83<h3>Method Details</h3>
84<div class="method">
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame]85 <code class="details" id="list">list(readGroupSetId, targetBucketWidth=None, x__xgafv=None, end=None, start=None, referenceName=None, pageToken=None, pageSize=None)</code>
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]86 <pre>Lists fixed width coverage buckets for a read group set, each of which
87correspond to a range of a reference sequence. Each bucket summarizes
88coverage information across its corresponding genomic range.
89
90For the definitions of read group sets and other genomics resources, see
91[Fundamentals of Google
92Genomics](https://cloud.google.com/genomics/fundamentals-of-google-genomics)
93
94Coverage is defined as the number of reads which are aligned to a given
95base in the reference sequence. Coverage buckets are available at several
96precomputed bucket widths, enabling retrieval of various coverage 'zoom
97levels'. The caller must have READ permissions for the target read group
98set.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]99
100Args:
101 readGroupSetId: string, Required. The ID of the read group set over which coverage is requested. (required)
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]102 targetBucketWidth: string, The desired width of each reported coverage bucket in base pairs. This
103will be rounded down to the nearest precomputed bucket width; the value
104of which is returned as `bucketWidth` in the response. Defaults
105to infinity (each bucket spans an entire reference sequence) or the length
106of the target range, if specified. The smallest precomputed
107`bucketWidth` is currently 2048 base pairs; this is subject to
108change.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]109 x__xgafv: string, V1 error format.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]110 Allowed values
111 1 - v1 error format
112 2 - v2 error format
113 end: string, The end position of the range on the reference, 0-based exclusive. If
114specified, `referenceName` must also be specified. If unset or 0, defaults
115to the length of the reference.
116 start: string, The start position of the range on the reference, 0-based inclusive. If
117specified, `referenceName` must also be specified. Defaults to 0.
118 referenceName: string, The name of the reference to query, within the reference set associated
119with this query. Optional.
120 pageToken: string, The continuation token, which is used to page through large result sets.
121To get the next page of results, set this parameter to the value of
122`nextPageToken` from the previous response.
Sai Cheemalapati4ba8c232017-06-06 18:46:08 -0400[diff] [blame]123 pageSize: integer, The maximum number of results to return in a single page. If unspecified,
124defaults to 1024. The maximum value is 2048.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]125
126Returns:
127 An object of the form:
128
129 {
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]130 "nextPageToken": "A String", # The continuation token, which is used to page through large result sets.
131 # Provide this value in a subsequent request to return the next page of
132 # results. This field will be empty if there aren't any additional results.
133 "coverageBuckets": [ # The coverage buckets. The list of buckets is sparse; a bucket with 0
134 # overlapping reads is not returned. A bucket never crosses more than one
135 # reference sequence. Each bucket has width `bucketWidth`, unless
136 # its end is the end of the reference sequence.
137 { # A bucket over which read coverage has been precomputed. A bucket corresponds
138 # to a specific range of the reference sequence.
139 "meanCoverage": 3.14, # The average number of reads which are aligned to each individual
140 # reference base in this bucket.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]141 "range": { # A 0-based half-open genomic coordinate range for search requests. # The genomic coordinate range spanned by this bucket.
142 "start": "A String", # The start position of the range on the reference, 0-based inclusive.
143 "end": "A String", # The end position of the range on the reference, 0-based exclusive.
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]144 "referenceName": "A String", # The reference sequence name, for example `chr1`,
145 # `1`, or `chrX`.
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]146 },
147 },
148 ],
Sai Cheemalapatic30d2b52017-03-13 12:12:03 -0400[diff] [blame]149 "bucketWidth": "A String", # The length of each coverage bucket in base pairs. Note that buckets at the
150 # end of a reference sequence may be shorter. This value is omitted if the
151 # bucket width is infinity (the default behaviour, with no range or
152 # `targetBucketWidth`).
Takashi Matsuo06694102015-09-11 13:55:40 -0700[diff] [blame]153 }</pre>
154</div>
155
156<div class="method">
157 <code class="details" id="list_next">list_next(previous_request, previous_response)</code>
158 <pre>Retrieves the next page of results.
159
160Args:
161 previous_request: The request for the previous page. (required)
162 previous_response: The response from the request for the previous page. (required)
163
164Returns:
165 A request object that you can call 'execute()' on to request the next
166 page. Returns None if there are no more items in the collection.
167 </pre>
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